The State Department has instructed former Secretary Hillary Rodham Clinton go back to her Internet companies and try to recover email messages from any personal email accounts that she used during her time in government, saying it appears she didn’t turn over all of her documents.

In a letter to Clinton lawyer David E. Kendall, the department said it has become aware of messages Mrs. Clinton sent to other government officials in her first few months in office, but which she did not turn over as part of the more than 30,000 emails she did relinquish last December.

Mrs. Clinton had previously said she used a personal email account — the same one she kept as a senator — to do government business during the first couple of months she was at the State Department. Her campaign said she no longer had access to those messages.

But after some of those messages were produced from the Defense Department, the State Department realized it had a problem.